Summary of Study ST003210
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002001. The data can be accessed directly via it's Project DOI: 10.21228/M8ZJ84 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST003210 |
| Study Title | Untargeted metabolomics analysis on single cells and cell clusters of TNBC cell lines using mass spectrometry |
| Study Summary | Triple-negative breast cancer (TNBC) is more aggressive than other subtypes of breast cancer， and 40% of TNBC patients undergo recurrence and metastasis after treatments. In the metastasis process, clustered cancer cells (cell clusters) exhibited a higher ability of invasion and metastasis. On the other hand, metabolic reprogramming is closely related to the process of cancer metastasis. To explore the metabolic heterogeneity between single cells and cell clusters, mass spectrometry-based untargeted metabolomic analysis was performed on single cells and cell clusters constructed from two TNBC cell lines (MDA-MB-231 and MDA-MB-453). As a result, metabolic profiling between single cells and cell clusters were explored and metabolites contributing to cell clustering were identified. |
| Institute | Nanjing Medical University |
| Last Name | Wang |
| First Name | Zhongcheng |
| Address | 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China |
| 1845775254@qq.com | |
| Phone | 025-86868326 |
| Submit Date | 2024-04-28 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-05-23 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002001 |
| Project DOI: | doi: 10.21228/M8ZJ84 |
| Project Title: | Untargeted metabolomics analysis on single cells and cell clusters of TNBC cell lines using mass spectrometry |
| Project Summary: | Single cells and cell clusters construcetd from two triple-negative breast cancer cell lines (MDA-MB-231 and MDA-MB-453) were used to screen differential metabolites. |
| Institute: | NanJing Medical University |
| Department: | School of Pharmacy |
| Last Name: | Wang |
| First Name: | Zhongcheng |
| Address: | 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China |
| Email: | 1845775254@qq.com |
| Phone: | 025-86868326 |
Subject:
| Subject ID: | SU003329 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Sample type |
|---|---|---|---|
| SA351494 | UM009 | Breast Cancer Cell Line | Blank |
| SA351495 | UM010 | Breast Cancer Cell Line | Blank |
| SA351496 | UM001 | Breast Cancer Cell Line | Blank |
| SA351497 | UM008 | Breast Cancer Cell Line | Blank |
| SA351498 | UM012 | Breast Cancer Cell Line | Blank |
| SA351499 | UM011 | Breast Cancer Cell Line | Blank |
| SA351500 | UM002 | Breast Cancer Cell Line | Blank |
| SA351501 | UM007 | Breast Cancer Cell Line | Blank |
| SA351502 | UM003 | Breast Cancer Cell Line | Blank |
| SA351503 | UM004 | Breast Cancer Cell Line | Blank |
| SA351504 | UM006 | Breast Cancer Cell Line | Blank |
| SA351505 | UM005 | Breast Cancer Cell Line | Blank |
| SA351506 | UM040 | Breast Cancer Cell Line | Cell_cluster |
| SA351507 | UM041 | Breast Cancer Cell Line | Cell_cluster |
| SA351508 | UM042 | Breast Cancer Cell Line | Cell_cluster |
| SA351509 | UM039 | Breast Cancer Cell Line | Cell_cluster |
| SA351510 | UM035 | Breast Cancer Cell Line | Cell_cluster |
| SA351511 | UM043 | Breast Cancer Cell Line | Cell_cluster |
| SA351512 | UM036 | Breast Cancer Cell Line | Cell_cluster |
| SA351513 | UM037 | Breast Cancer Cell Line | Cell_cluster |
| SA351514 | UM038 | Breast Cancer Cell Line | Cell_cluster |
| SA351515 | UM051 | Breast Cancer Cell Line | Cell_cluster |
| SA351516 | UM050 | Breast Cancer Cell Line | Cell_cluster |
| SA351517 | UM034 | Breast Cancer Cell Line | Cell_cluster |
| SA351518 | UM052 | Breast Cancer Cell Line | Cell_cluster |
| SA351519 | UM049 | Breast Cancer Cell Line | Cell_cluster |
| SA351520 | UM048 | Breast Cancer Cell Line | Cell_cluster |
| SA351521 | UM045 | Breast Cancer Cell Line | Cell_cluster |
| SA351522 | UM046 | Breast Cancer Cell Line | Cell_cluster |
| SA351523 | UM047 | Breast Cancer Cell Line | Cell_cluster |
| SA351524 | UM044 | Breast Cancer Cell Line | Cell_cluster |
| SA351525 | UM031 | Breast Cancer Cell Line | Cell_cluster |
| SA351526 | UM018 | Breast Cancer Cell Line | Cell_cluster |
| SA351527 | UM033 | Breast Cancer Cell Line | Cell_cluster |
| SA351528 | UM020 | Breast Cancer Cell Line | Cell_cluster |
| SA351529 | UM021 | Breast Cancer Cell Line | Cell_cluster |
| SA351530 | UM017 | Breast Cancer Cell Line | Cell_cluster |
| SA351531 | UM016 | Breast Cancer Cell Line | Cell_cluster |
| SA351532 | UM013 | Breast Cancer Cell Line | Cell_cluster |
| SA351533 | UM014 | Breast Cancer Cell Line | Cell_cluster |
| SA351534 | UM015 | Breast Cancer Cell Line | Cell_cluster |
| SA351535 | UM022 | Breast Cancer Cell Line | Cell_cluster |
| SA351536 | UM019 | Breast Cancer Cell Line | Cell_cluster |
| SA351537 | UM030 | Breast Cancer Cell Line | Cell_cluster |
| SA351538 | UM023 | Breast Cancer Cell Line | Cell_cluster |
| SA351539 | UM032 | Breast Cancer Cell Line | Cell_cluster |
| SA351540 | UM028 | Breast Cancer Cell Line | Cell_cluster |
| SA351541 | UM029 | Breast Cancer Cell Line | Cell_cluster |
| SA351542 | UM024 | Breast Cancer Cell Line | Cell_cluster |
| SA351543 | UM027 | Breast Cancer Cell Line | Cell_cluster |
| SA351544 | UM025 | Breast Cancer Cell Line | Cell_cluster |
| SA351545 | UM026 | Breast Cancer Cell Line | Cell_cluster |
| SA351546 | UM068 | Breast Cancer Cell Line | QCs |
| SA351547 | UM067 | Breast Cancer Cell Line | QCs |
| SA351548 | UM066 | Breast Cancer Cell Line | QCs |
| SA351549 | UM065 | Breast Cancer Cell Line | QCs |
| SA351550 | UM064 | Breast Cancer Cell Line | QCs |
| SA351551 | UM072 | Breast Cancer Cell Line | QCs |
| SA351552 | UM071 | Breast Cancer Cell Line | QCs |
| SA351553 | UM070 | Breast Cancer Cell Line | QCs |
| SA351554 | UM069 | Breast Cancer Cell Line | QCs |
| SA351555 | UM057 | Breast Cancer Cell Line | QCs |
| SA351556 | UM056 | Breast Cancer Cell Line | QCs |
| SA351557 | UM055 | Breast Cancer Cell Line | QCs |
| SA351558 | UM054 | Breast Cancer Cell Line | QCs |
| SA351559 | UM063 | Breast Cancer Cell Line | QCs |
| SA351560 | UM058 | Breast Cancer Cell Line | QCs |
| SA351561 | UM053 | Breast Cancer Cell Line | QCs |
| SA351562 | UM062 | Breast Cancer Cell Line | QCs |
| SA351563 | UM059 | Breast Cancer Cell Line | QCs |
| SA351564 | UM061 | Breast Cancer Cell Line | QCs |
| SA351565 | UM060 | Breast Cancer Cell Line | QCs |
| SA351566 | UM099 | Breast Cancer Cell Line | Single_cell |
| SA351567 | UM102 | Breast Cancer Cell Line | Single_cell |
| SA351568 | UM101 | Breast Cancer Cell Line | Single_cell |
| SA351569 | UM100 | Breast Cancer Cell Line | Single_cell |
| SA351570 | UM097 | Breast Cancer Cell Line | Single_cell |
| SA351571 | UM103 | Breast Cancer Cell Line | Single_cell |
| SA351572 | UM095 | Breast Cancer Cell Line | Single_cell |
| SA351573 | UM096 | Breast Cancer Cell Line | Single_cell |
| SA351574 | UM098 | Breast Cancer Cell Line | Single_cell |
| SA351575 | UM108 | Breast Cancer Cell Line | Single_cell |
| SA351576 | UM110 | Breast Cancer Cell Line | Single_cell |
| SA351577 | UM111 | Breast Cancer Cell Line | Single_cell |
| SA351578 | UM112 | Breast Cancer Cell Line | Single_cell |
| SA351579 | UM109 | Breast Cancer Cell Line | Single_cell |
| SA351580 | UM094 | Breast Cancer Cell Line | Single_cell |
| SA351581 | UM105 | Breast Cancer Cell Line | Single_cell |
| SA351582 | UM106 | Breast Cancer Cell Line | Single_cell |
| SA351583 | UM107 | Breast Cancer Cell Line | Single_cell |
| SA351584 | UM104 | Breast Cancer Cell Line | Single_cell |
| SA351585 | UM088 | Breast Cancer Cell Line | Single_cell |
| SA351586 | UM078 | Breast Cancer Cell Line | Single_cell |
| SA351587 | UM079 | Breast Cancer Cell Line | Single_cell |
| SA351588 | UM080 | Breast Cancer Cell Line | Single_cell |
| SA351589 | UM081 | Breast Cancer Cell Line | Single_cell |
| SA351590 | UM077 | Breast Cancer Cell Line | Single_cell |
| SA351591 | UM076 | Breast Cancer Cell Line | Single_cell |
| SA351592 | UM073 | Breast Cancer Cell Line | Single_cell |
| SA351593 | UM074 | Breast Cancer Cell Line | Single_cell |
Collection:
| Collection ID: | CO003322 |
| Collection Summary: | Two hours before metabolite extraction, the cell culture medium was replaced with fresh medium. Single cell and cell cluster states were collected and centrifuged at 800 × g for 3 min to remove culture media. Then, the cells were resuspended in 1 mL of precooled PBS (4°C) and transferred into a 1.5 mL eppendorf tube. After removing supernatant by centrifugation at 800 × g for 3 min, the tube containing cell pellet was immediately incubated in liquid nitrogen for 1 min to quench enzyme activity and stop the degradation of metabolites. |
| Collection Protocol Filename: | WZC_Collection_protocol.pdf |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR003338 |
| Treatment Summary: | MDA-MB-231 cells and MDA-MB-453 were maintained in L-15 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37 °C in a free gas exchange with atmospheric air. |
Sample Preparation:
| Sampleprep ID: | SP003336 |
| Sampleprep Summary: | 300 μL of H2O was then added to the tube, and the cells were fully lysed by an ultrasonic cell disruptor for 10 min at 4°C. After mixing, 20 μL of suspension was collected for protein quantification and subsequent data normalization. Then, methanol (precooled to −80°C) was added into the tube to make 80% methanol solution (v/v). The tube was vortexed vigorously for 5 min and centrifuged at 14,000 × g for 10 min at 4°C to remove the cell debris. Afterward, the metabolite-containing supernatant was transferred to a new tube on ice. The supernatant was evaporated to dryness in a vacuum concentrator and reconstituted in 100 μL of methanol: H2O (1:1, v/v), which was centrifuged again at 14000 × g for 15 min at 4°C to remove insoluble debris. |
| Sampleprep Protocol Filename: | Sampleprep_protocol.pdf |
Combined analysis:
| Analysis ID | AN005262 | AN005263 | AN005264 | AN005265 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | HILIC | HILIC | Reversed phase | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Agilent InfinityLab Poroshell 120 HILIC-Z (100 x 2.1mm, 2.7um) | Agilent InfinityLab Poroshell 120 HILIC-Z (100 x 2.1mm, 2.7um) | Phenomenex Kinetex C18 (100 x 2.1mm,2.6um) | Phenomenex Kinetex C18 (100 x 2.1mm,2.6um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | Peak area | Peak area | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH003983 |
| Methods Filename: | Chromatography_methods.pdf |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Agilent InfinityLab Poroshell 120 HILIC-Z (100 x 2.1mm, 2.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | 85% B (0 min) to 85% B (1 min) to 65% B (12 min) to 40% B (12.1 min) to 40% B (15 min) to 85% B (15.1 min) to 85% B (20 min), the flow gradient increases linearly between the time points mentioned. |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 100% Water; 25 mM Ammonium acetate; 25 mM Ammonium hydroxide |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH003984 |
| Methods Filename: | Chromatography_methods.pdf |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Phenomenex Kinetex C18 (100 x 2.1mm,2.6um) |
| Column Temperature: | 40 |
| Flow Gradient: | 10% B (0 min) to 30% B (1 min) to 95% B (19 min) to 95% B (20 min) to 10% B (20.1 min) to 10% B (23 min), the flow gradient increases linearly between the time points mentioned. |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 100% Water; 0.1% Formic acid |
| Solvent B: | 100% Acetonitrile; 0.1% Formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004993 |
| Analysis ID: | AN005262 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | All operations and acquisitions were controlled by Xcalibur 2.0.7 (Thermo Fisher Scientific, Bremen, Germany).UPLC-HRMS data were analyzed using MS-DIAL software after conversion to mzML file format using MSConvert (Version 3.0, ProteiWizard). |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | MS_analysis_protocol.pdf |
| MS ID: | MS004994 |
| Analysis ID: | AN005263 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | All operations and acquisitions were controlled by Xcalibur 2.0.7 (Thermo Fisher Scientific, Bremen, Germany).UPLC-HRMS data were analyzed using MS-DIAL software after conversion to mzML file format using MSConvert (Version 3.0, ProteiWizard). |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | MS_analysis_protocol.pdf |
| MS ID: | MS004995 |
| Analysis ID: | AN005264 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | All operations and acquisitions were controlled by Xcalibur 2.0.7 (Thermo Fisher Scientific, Bremen, Germany).UPLC-HRMS data were analyzed using MS-DIAL software after conversion to mzML file format using MSConvert (Version 3.0, ProteiWizard). |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | MS_analysis_protocol.pdf |
| MS ID: | MS004996 |
| Analysis ID: | AN005265 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | All operations and acquisitions were controlled by Xcalibur 2.0.7 (Thermo Fisher Scientific, Bremen, Germany).UPLC-HRMS data were analyzed using MS-DIAL software after conversion to mzML file format using MSConvert (Version 3.0, ProteiWizard). |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | MS_analysis_protocol.pdf |
